By God's help, I will reply to these claims, and I may start by this one:
Scientific Errors in the Qur'an - WikiIslam
The answer is here:
The Universe and the Quran 3
Question 42: What is meant by His saying – be glorified – in the Quran 18: 86, which means:
(Until when he reached at sun-set [time], he found it setting under the observation of a black woman, and he found with her a people.)
(We said, “O Zul-qarnain, you have either to punish or to show them kindness.) ?
Answer: When Alexander of Macedon reached the West, i.e. to Abyssinia, he found the citizens of that country worshipping the sun, so that they gathered outside the city at the time of sun-set, looked to the sun and sung their religious songs, and when it was about to set down and disappear from sight behind the horizon, they would kneel down and adore the sun, all of them. They had a black queen in front of them, who led them in prayer, and they imitated her prayer to the sun.
The interpretation:
>> (Until when he) i.e. Alexander (reached)
>> (at sun-set [time] ) means: He arrived, at that place, at the time of sun-set.
>> (he found it setting under the observation of a black woman) means: He found a black woman watching the sun, while it was setting. That woman was a queen; and her people were assembling with her.
The meaning: Alexander found a people worshipping the sun at its setting; they had a queen leading them in prayer to the sun; she was adoring and kneeling down to the sun; so that her people were imitating her, and doing the same as was their queen doing.
In Arabic, the word عين was misinterpreted as the ‘water-spring’; while, actually, it means the ‘watching and observation’; as is it mentioned in many instances in the Quran and in the Arab poetry. Examples:
(1) God - be exalted - said in the Quran 11: 37, which means:
(But build the Ark under Our observation and as We instruct you by revelation.)
(2) God – be highly exalted - said in the Quran, 54:14, which means:
(Which ran [upon the water,] in Our sight, as a reward for him that was rejected ) i.e. under Our watching and observation.
(3) God - be exalted – said also in the Quran, 52: 48, which means:
(So forbear patiently to the commandment of your Lord: for surely you [Mohammed] are under Our observation. And celebrate the praises of your Lord, when you rise up [from sleep.] )
His saying -be exalted - (for surely you [Mohammed] are under Our observation.) means: under Our observation and watching.
[Now we continue the interpretation of the Quranic revelation 18: 87-88]
>> (and he found with her a people.) means: Alexander found, with the black woman, a people doing exactly as was she doing, and imitating her in her worship.
>> (We said, “O Zul-qarnain); this is the surname or the title of Alexander.
>> (you have either to punish) these people who are worshipping the sun, if they do not believe in God and resign or submit themselves to Him.
>> (or to show them kindness) if they believe and obey Our order.
Here, the عين in Arabic means the watching, and it does not mean a water-spring. The proof of this lies in His saying -be exalted - in the Quran 18: 91, which means:
(Until when he reached at sun-rising [time], he found it rise upon a people for whom We made no shelter therefrom.)
So, if the عين meant a water-spring, then God – be glorified – would say: ‘he found it rise from a water-spring!’ But the meaning is: He found it set down for a people having such a description; and rise upon a people having such a description.
Therefore, God - be exalted – meant by that to describe the people, and not to describe the sun.
[This also is the meaning of the word in the Arab poetry, some of which is mentioned by the late Mohammed-Ali Hassan, the interpreter of the Quran and the Bible, in his Arabic book.]